Details
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Type: Bug
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Status: Closed
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Priority: Major
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Resolution: Fixed
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Affects Version/s: None
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Fix Version/s: 2.11.1.1
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Component/s: Command Line Interface
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Labels:None
Description
Jalview reports 'Can't find https:...' when -headless used and it is asked to open a url with protocol other than http://
(base) ls30857-3:jalview jprocter$ jalview -headless -open https://www.jalview.org/examples/uniref50.fa
Running jalview.bin.Jalview with -Xmx15461881856
Java version: 12
Java Home: /Library/Java/JavaVirtualMachines/adoptopenjdk-12.jdk/Contents/Home
x86_64 Mac OS X 10.13.6
Jalview Version: 2.11.1.0 (bioconda (build 0) git-commit: [])
Quaqua LaF not available on this plaform. Using VAqua(4).
See https://issues.jalview.org/browse/JAL-2976
Ignoring SO:0001957 as obsolete and duplicated by SO:0001979
Ignoring SO:0000437 as obsolete and duplicated by SO:0000800
Ignoring SO:0000554 as obsolete and duplicated by SO:0000801
Ignoring SO:0000767 as obsolete and duplicated by SO:0000179
Ignoring SO:0000058 as obsolete and duplicated by SO:0000803
Ignoring SO:0001052 as obsolete and duplicated by SO:0001649
Ignoring SO:0000052 as obsolete and duplicated by SO:0000802
Ignoring SO:0001053 as obsolete and duplicated by SO:0001648
Loaded Sequence Ontology from so-xp-simple.obo.zip (199ms)
CMD [-open https://www.jalview.org/examples/uniref50.fa] executed successfully!
Can't find https://www.jalview.org/examples/uniref50.fa
But:
(base) ls30857-3:jalview jprocter$ curl https://www.jalview.org/examples/uniref50.fa
>FER_CAPAA Ferredoxin
-----------------------------------------------------------ASYKVKLITPDGP
IEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV
(base) ls30857-3:jalview jprocter$ jalview -headless -open https://www.jalview.org/examples/uniref50.fa
Running jalview.bin.Jalview with -Xmx15461881856
Java version: 12
Java Home: /Library/Java/JavaVirtualMachines/adoptopenjdk-12.jdk/Contents/Home
x86_64 Mac OS X 10.13.6
Jalview Version: 2.11.1.0 (bioconda (build 0) git-commit: [])
Quaqua LaF not available on this plaform. Using VAqua(4).
See https://issues.jalview.org/browse/JAL-2976
Ignoring SO:0001957 as obsolete and duplicated by SO:0001979
Ignoring SO:0000437 as obsolete and duplicated by SO:0000800
Ignoring SO:0000554 as obsolete and duplicated by SO:0000801
Ignoring SO:0000767 as obsolete and duplicated by SO:0000179
Ignoring SO:0000058 as obsolete and duplicated by SO:0000803
Ignoring SO:0001052 as obsolete and duplicated by SO:0001649
Ignoring SO:0000052 as obsolete and duplicated by SO:0000802
Ignoring SO:0001053 as obsolete and duplicated by SO:0001648
Loaded Sequence Ontology from so-xp-simple.obo.zip (199ms)
CMD [-open https://www.jalview.org/examples/uniref50.fa] executed successfully!
Can't find https://www.jalview.org/examples/uniref50.fa
But:
(base) ls30857-3:jalview jprocter$ curl https://www.jalview.org/examples/uniref50.fa
>FER_CAPAA Ferredoxin
-----------------------------------------------------------ASYKVKLITPDGP
IEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV